[BioC] RMA error in cdf environment with removed probes (Yeast2)

[Jenny Drnevich]

Hi Omri,

I'm assuming that the RemoveProbes.r function is the one I have 
posted to the Bioconductor mailing list several times, mostly 
recently with some changes on Sept 24, 2008? 
https://stat.ethz.ch/pipermail/bioconductor/2008-September/024296.html

If so, would you post your entire session, including the code you 
used to remove the probe sets and probes, along with your 
sessionInfo()? That should give us more details so we can help you.

Thanks,
Jenny

At 10:08 PM 12/16/2008, Omri Yahel wrote:
>Hello
>
>I am encountering an error during RMA of an affybatch.
>I have used RemoveProbes.r to remove all S. pombe probesets and 864
>individual S.cerevisiae probes from the yeast2 platform.
>
> >data<-ReadAffy()
> > data
>AffyBatch object
>size of arrays=496x496 features (11 kb)
>cdf=Yeast_2 (5900 affyids)
>number of samples=26
>number of genes=5900
>annotation=yeast2
>notes=
> >
> > length(pm(data[,1]))
>[1] 64688
>
>
>When I attempt to compute the eset
>
> > eset <- rma(data)
>Background correcting
>Normalizing
>Calculating Expression
>Error in rma(data) : length of 'dimnames' [1] not equal to array extent
>
>I assume this has something to do with the removal of individual probes from
>the environment, but am not sure and do not know how to remedy this.
>Any help appreciated
>
>Omri Yahel
>MSc student
>School of Biological Sciences
>University of Auckland, New Zealand
>
>         [[alternative HTML version deleted]]
>
>_______________________________________________
>Bioconductor mailing list
>Bioconductor at stat.math.ethz.ch
>https://stat.ethz.ch/mailman/listinfo/bioconductor
>Search the archives: 
>http://news.gmane.org/gmane.science.biology.informatics.conductor

Jenny Drnevich, Ph.D.

Functional Genomics Bioinformatics Specialist
W.M. Keck Center for Comparative and Functional Genomics
Roy J. Carver Biotechnology Center
University of Illinois, Urbana-Champaign

330 ERML
1201 W. Gregory Dr.
Urbana, IL 61801
USA

ph: 217-244-7355
fax: 217-265-5066
e-mail: drnevich at illinois.edu